It wasn't for rhetorical effect, it is the basis of his argument against physcalism. What he is saying, as Loseyourname said, is that physics studies the relations between things, not the things themselves. In other words, physics has no grounding ontology.
This is equivalent to saying that the universe of subjects and objects has only a dependent existence or, more scientifically, as Bohm and others argue, that it is in effect a hologram. I don't know Bohm well but perhaps one could say that physics studies what is explicate, not what is implicate. Note also that in M-theory there is a sense in which spacetime, and thus all it contains, does not exist. Physics has yet to identify any absolute substance or entity. In more philosophical terms we could say that we still cannot see beyond appearances, or out of Plato's cave, or solve the problem of attributes (of what exists other than appearances).
This is what the issue of bare differences is about. What GR is saying is that physics cannot provide a complete ontological account of the universe, an account of what things actually are, because it studies only the difference between things, not the things themselves. These differences are 'bare' in the sense that they are not ontological differences but simply differences in the appearance of things. In a way this is just a restatement of the 'hard problem' in a different form. GR relates this to the problematic ontology of conscious experience, but it is just relevant to the problematic ontology of matter and energy.
On the biology/life question you might be interested in Varella's work on autopoetic systems. He examines their structure and emergence in the light of the mathematics of George Spencer-Brown, which is founded on the proposition that such structures arise from and consist of, in effect, just bare differences.